The Permissions & webhooks page of the GitHub App settings says that current users will be prompted to accept new changes to permissions. But are users prompted to accept changes to webhooks as well?
The webhooks you can listen on are nested under their respective permissions.
A change in permissions will prompt users to accept changes. If you change permissions AND webhooks that will also prompt users to accept. A change in only webhooks will NOT prompt users since you already have the permission associated with that webhook.